Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

Pös, Zuzana; Pös, Ondrej; Styk, Jakub; Mocova, Angelika; Striešková, Lucia; Budiš, Jaroslav; Kádaši, Ľudevít; Radvánszky, Ján; Szemes, Tomáš

doi:10.3390/ijms21228634

Cited by 38 publications

(31 citation statements)

References 328 publications

(306 reference statements)

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“…Tubes containing specific preservatives should be used whenever it is not possible to process the sample within 3 h from collection. 11 , 12 …”

Section: Technical Aspectsmentioning

confidence: 99%

The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

Russo¹,

Incorvaia²,

Re³

et al. 2021

ESMO Open

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The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts’ opinions, the AIOM–SIAPEC-IAP–SIBIOC–SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting.

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“…Tubes containing specific preservatives should be used whenever it is not possible to process the sample within 3 h from collection. 11 , 12 …”

Section: Technical Aspectsmentioning

confidence: 99%

The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

Russo¹,

Incorvaia²,

Re³

et al. 2021

ESMO Open

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“…Since tumor cells frequently undergo necrosis, they release tumor-specific cfDNA (ctDNA) into body fluids such as blood, urine, saliva, etc. [84]. It was shown that quantification of tumor-specific rearrangements in ctDNA by ddPCR is highly accurate for postsurgical discrimination between patients with an eventual diagnosis of clinical metastasis and long-term disease-free patients, with a sensitivity of 93% (95% CI, 66-100%) and specificity of 100% (95% CI, 61-100%).…”

Section: Potential Biomedical Applications Of Cnv Detectionmentioning

confidence: 99%

Copy Number Variation: Methods and Clinical Applications

et al. 2021

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Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases. In recent decades, researchers developed a wide variety of cytogenetic and molecular methods with different detection capabilities to detect clinically relevant CNVs. In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases. Although the recent rapid progress of sequencing methods has enabled precise detection of CNVs, determining their functional effect on cellular and whole-body physiology remains a challenge. Here, we provide a comprehensive list of databases and bioinformatics tools that may serve as useful assets for researchers, laboratory diagnosticians, and clinical geneticists facing the challenge of CNV detection and interpretation.

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“…In addition to sample considerations, there is a need for standardized sampling and processing techniques with respect to liquid profiling of nucleic acids [ 36 , 37 ]. Fortunately, the World Health Organization specifies collection standards for blood and CSF [ 38 , 39 ].…”

Section: Main Textmentioning

confidence: 99%

Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics

et al. 2021

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Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.

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Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

Cited by 38 publications

References 328 publications

The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

Copy Number Variation: Methods and Clinical Applications

Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics

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